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Fig. 4 | BMC Biology

Fig. 4

From: High-resolution structure of the amino acid transporter AdiC reveals insights into the role of water molecules and networks in oligomerization and substrate binding

Fig. 4

Orientation of gating residues W202 and W293 in the AdiC crystal structure and molecular dynamics (MD) simulations analysis. A Side view of the AdiC dimer structure (monomers in yellow and light blue) as seen from the membrane plane. The regions containing the proximal W202 and middle W293 gates are highlighted with a red and black square, respectively. B Hydrogen bond interactions observed between the W202 nitrogen atom, three water molecules (α, β and γ), and main and side chain atoms are shown as dashed lines and distances are indicated in Å. Hydrophobic residues (I205, V358, I359, and L362) interacting with W202 within ≤ 4 Å are displayed. C Water molecule H2O9 mediated hydrogen bonds between the more buried middle gate residue W293, and S298 and N22(O) are shown as dashed lines and distances are indicated in Å. Residues (N22, I205, G206, L296) interacting with W293 within ≤ 4 Å are displayed. Waters are depicted as orange spheres and amino acids are colored in blue (main chain interactions) and cyan (side chain interactions). Amino acids are labeled in the one letter code whereas main chain interactions with the carbonyl oxygen or nitrogen atom are additionally labeled with (O) or (N). D, E Selected conformations of the W202 (D) and W293 (E) side chains from MD simulations. W202 and W293 are displayed in red and green hues, respectively. The W202 and W293 conformations found in the crystal structure are colored in black

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